SCIENTIFIC REPORT 2004 - Sylvester Comprehensive Cancer Center

T U M O R C E L L B I O L O G Y P R O G R A M
HIGHLIGHTS/DISCOVERIES
• Developed the HA-HAase urine test, a noninvasive
test that is about 90 percent accurate in
detecting bladder cancer and monitoring its
recurrence.
• Established that HA and HAase are greater than
85 percent accurate prognostic indicators for
prostate cancer.
• Demonstrated the function of tumor-derived
HAase in bladder tumor growth and muscle
invasion.
ARUN MALHOTRA, PH.D.
Assistant Professor of Biochemistry and
Molecular Biology
DESCRIPTION OF RESEARCH
Dr. Malhotra’s research interests lie in structural
biology of macromolecules involved in
a variety of basic cellular functions. Three major
areas of research include bacterial nucleases
involved in RNA maturation and degradation,
enzymes involved in RNA modification, and
molecules involved in axonal guidance and
neuronal development. These macromolecules
are being studied using the tools of X-ray crystallography
and molecular biology.
Bacterial Exoribonucleases
Ribonucleases play a central role in vital cellular
RNA processes such as mRNA degradation and
maturation and turnover of stable RNAs. Eight
distinct exoribonucleases have been identified in
E. coli. Of these, three (RNase T, RNase D, and
oligoribonuclease) are members of a larger exonuclease
superfamily (named the DEDD exonuclease
family, after the four invariant acidic
residues in these proteins) that includes the
proofreading domains of DNA polymerases.
While these proteins share similar sequence
motifs, they are functionally quite different.
RNase T is involved in tRNA turnover and maturation
of tRNAs, 23S, and 5S rRNAs. RNase D
also is involved in the maturation of tRNAs and
small RNAs, but mainly as a backup enzyme.
RNase D functions as a monomer, while RNase
T and oligoribonuclease exist as dimers.
Oligoribonuclease catalyzes the degradation of
very short RNAs and is the only exoribonuclease
essential for cell viability in E. coli.
This project aims to obtain structures of
these three exoribonucleases and to compare
them to better understand differences in substrate
specificities. The long-term goal of this research is
to understand the structures and mechanisms of
action of all exoribonucleases in a single organism;
this study complements a parallel study under
way in the laboratory of Murray P. Deutscher,
Ph.D., (University of Miami), to completely
characterize the physiological role of all the
exoribonucleases in E. coli.
Pseudouridine Synthases
One of the most abundant post-transcriptional
modifications seen in RNA is the isomerization
of uridine to pseudouridine (5-ribosyluracil).
While the physiological role of this modification
in cells is not yet well understood, pseudouridines
are often seen in functionally important regions
of structural RNAs such as ribosomal RNAs,
transfer RNAs, and splicing RNAs.
The isomerization of uridines to pseudouridines
is carried out by specialized enzymes called
pseudouridine synthases. These enzymes fall into
five different families; crystallographic studies in
a number of laboratories have shown that three of
these families have very similar structures in spite
of limited sequence homologies. This project
focuses on the structural studies of pseudouridine
synthases from the other two families (RluD from
the RluA family, and the newly discovered TruD
family), in collaboration with the laboratory of E.
James Ofengand, Ph.D., (University of Miami).
Structural Studies of Axonal Guidance
Molecules
Research in this area aims to structurally characterize
the interactions between ephrins and their
receptors, a class of molecules involved in axonal
guidance in the developing nervous system. Apart
from axonal guidance, these receptors/ligands
UM/Sylvester Comprehensive Cancer Center Scientific Report 2004 87